Dear Freesurfer Experts,

I am trying to create surfaces that can be used in afni/SUMA for cortical based inter-subject alignment. For most of my subjects your programs have worked perfectly. But I am having a problem for two subjects with dura residual from the skull stripping that is disotrting the pial surface and produces long protruding 'handles' stemming from the cortial surface once generated in SUMA. I have made edits to the offending voxels in the brainmask.mgz using tkmedit according to the tutorial, and subsequently re-run recon-all -autorecon2-pial -autorecon3 -subjid subj05, but the surfaces still appear as they were prior to the edits. I looked at the brain.finalsurfs and noticed that the red and yellow lines demarcating WM and pial surfaces where I had deleted offending voxels remain despite re-running recon-all, as if new surfaces had not been generated. Can you tell me what I am doing wrong? Is it possible to edit the offending surface markers themselves? Any help and advice woudl be greatly appreciated.

~michael

Systems Neuroscience, NIN Universitatsklinikum Hamburg-Eppendorf

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